1-100611655-T-C

Position:

• chr1-100611655-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.209 in 152,014 control chromosomes in the GnomAD database, including 3,447 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (3447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31715 AN: 151896 Hom.: 3440 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.242

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.209 AC: 31741 AN: 152014 Hom.: 3447 Cov.: 32 AF XY: 0.210 AC XY: 15633 AN XY: 74286

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.241

Alfa AF: 0.194 Hom.: 449

Bravo AF: 0.207

Asia WGS AF: 0.180 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	20
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2027166; hg19: chr1-101077211;